QBiC

Project Members:

Prof. Dr. Verena Keitel

verena.keitel@med.uni-duesseldorf.de

Universitätsklinikum Düsseldorf


Dr. Maria Reich

maria.reich@uni-duesseldorf.de

Universitätsklinikum Düsseldorf


Prof. Dr. Mathias Heikenwälder

m.heikenwaelder@dkfz-heidelberg.de

DKFZ Heidelberg




QBiC contacts:

Dr. Gisela Gabernet

Bioinformatics project manager

gisela.gabernet@qbic.uni-tuebingen.de

1 Pathway analysis

The pathway analysis results are stored here, and explained in this section.

1.1 Enriched pathways plot

The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value < 0.05). Only contrasts for which an enriched pathway was found are shown. Both KEGG pathways and REACTOME (REAC) pathways were considered.

Hover over the dots to reveal the pathway names.

1.2 Enriched pathways table

Table summarizing all the enriched pathways. The results can also be inspected on the browser query under this link: https://biit.cs.ut.ee/gplink/l/VMSJLd0yTj. This table can be also found under pathway_analysis.

Contrast Pathway name Pathway code DE genes in pathway (N) Total genes in pathway (N) Fraction of DE genes in pathway Padj value (pathway enrichment) DE genes names
DE_genes_Cholangiocytes_KO_vs_WT Complement and coagulation cascades KEGG:04610 15 91 0.165 1e-07 C3,Serpina1b,Serpina1a,Serpina1d,Serpind1,Serpina1c,Cfb,Cpb2,F2,Vtn,Kng2,C4bp,Fgg,Cfi,Fga
DE_genes_Cholangiocytes_KO_vs_WT Steroid biosynthesis KEGG:00100 7 20 0.35 1.29e-05 Sqle,Cyp51,Fdft1,Msmo1,Nsdhl,Dhcr7,Sc5d
DE_genes_Cholangiocytes_KO_vs_WT Terpenoid backbone biosynthesis KEGG:00900 6 23 0.261 0.000731 Hmgcr,Fdps,Idi1,Hmgcs1,Mvd,Pmvk
DE_genes_Cholangiocytes_KO_vs_WT Cell adhesion molecules KEGG:04514 13 162 0.0802 0.00541 Cldn10,Cldn8,H2-T23,H2-Q6,H2-D1,H2-Q7,H2-K1,Cldn2,Cdh2,Vcam1,Itgav,Icam1,Cldn4
DE_genes_Cholangiocytes_KO_vs_WT Human T-cell leukemia virus 1 infection KEGG:05166 15 236 0.0636 0.0209 Fdps,H2-T23,H2-Q6,H2-D1,H2-Q7,H2-K1,Ccnd2,Creb3l3,Zfp36,Tgfb2,Ran,Tspo,Trp53,Nfkbia,Icam1
DE_genes_Cholangiocytes_KO_vs_WT Kaposi sarcoma-associated herpesvirus infection KEGG:05167 14 217 0.0645 0.029 C3,H2-T23,H2-Q6,Ubc,H2-D1,Vegfa,H2-Q7,H2-K1,Stat1,Zfp36,Trp53,Ifngr1,Nfkbia,Icam1
DE_genes_Cholangiocytes_KO_vs_WT AGE-RAGE signaling pathway in diabetic complications KEGG:04933 9 99 0.0909 0.03 Vegfa,Ccl2,Stat1,Vcam1,Tgfb2,Fn1,Agt,Icam1,Col4a1
DE_genes_Cholangiocytes_KO_vs_WT Proteasome KEGG:03050 6 47 0.128 0.05 Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Cholesterol biosynthesis REAC:R-MMU-191273 12 25 0.48 6.84e-12 Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Nsdhl,Dhcr7,Mvd,Pmvk,Sc5d
DE_genes_Cholangiocytes_KO_vs_WT Metabolism of steroids REAC:R-MMU-8957322 20 122 0.164 2.15e-10 Gc,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Nsdhl,Dhcr7,Srebf2,Mvd,Pmvk,Sc5d,Alb,Serpina6,Akr1c6,Ran,Tspo,Hsd17b2
DE_genes_Cholangiocytes_KO_vs_WT Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 19 111 0.171 3.75e-10 Trf,C3,Igfbp4,Serpina10,Igfbp5,Gas6,Ahsg,Lgals1,Alb,Serpind1,Shisa5,Apob,Cdh2,Csf1,Kng2,Fgg,Fn1,Fga,Igf1
DE_genes_Cholangiocytes_KO_vs_WT Post-translational protein phosphorylation REAC:R-MMU-8957275 18 105 0.171 1.48e-09 Trf,C3,Igfbp4,Serpina10,Igfbp5,Gas6,Ahsg,Lgals1,Alb,Serpind1,Shisa5,Apob,Cdh2,Csf1,Kng2,Fgg,Fn1,Fga
DE_genes_Cholangiocytes_KO_vs_WT Platelet degranulation REAC:R-MMU-114608 16 110 0.145 3.04e-07 Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1
DE_genes_Cholangiocytes_KO_vs_WT Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 16 115 0.139 5.95e-07 Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1
DE_genes_Cholangiocytes_KO_vs_WT Metabolism of lipids REAC:R-MMU-556833 34 583 0.0583 1.3e-05 Gc,Tbxas1,Fads1,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Scd2,Nsdhl,Elovl6,Dhcr7,Srebf2,Dbi,Degs2,Mvd,Mid1ip1,Pmvk,Sc5d,Gpx4,Cyp2d22,Alb,Serpina6,Gpx1,Hsd17b13,Akr1c6,Ran,Tspo,Plpp3,Fabp5,Hsd17b2,Ephx2
DE_genes_Cholangiocytes_KO_vs_WT Innate Immune System REAC:R-MMU-168249 45 976 0.0461 7.06e-05 Txnip,Pigr,C3,Anpep,H2-T23,Ahsg,Hp,H2-Q6,Crp,Cystm1,Ubc,Mme,Psmd8,Hspa8,H2-Q7,Cstb,Ctsh,H2-K1,Cfb,Nme2,Apob,Cpb2,Dynll1,F2,Atox1,Vtn,Psmb3,Psmb2,Psmb1,Psmb5,Bst2,Psma3,Mif,C4bp,Fgg,Tubb5,Fabp5,Cfi,Birc2,Fga,Lcn2,Itgav,Cpn1,Nfkbia,Stbd1
DE_genes_Cholangiocytes_KO_vs_WT Metabolism REAC:R-MMU-1430728 63 1678 0.0375 0.00026 Gc,Tbxas1,Fads1,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Scd2,Nsdhl,Elovl6,Dhcr7,Srebf2,Bgn,Dbi,Degs2,Mvd,Ces1d,Aldh1l1,Mid1ip1,Rbp1,Pmvk,Sc5d,Psmd8,Gpx4,Cyp2d22,Aldh1a1,Ndufa6,Slc2a2,Aldob,Alb,Cbs,Adk,St3gal4,Nme2,Serpina6,Gpx1,Apob,Qprt,Glo1,Psmb3,Fbp1,Nme1,Ces3a,Hsd17b13,Psmb2,Akr1c6,Psmb1,Psmb5,Nostrin,Ran,Psma3,Ext1,Tspo,Plpp3,Fabp5,Ddah1,Tst,Hsd17b2,Ephx2,Gamt
DE_genes_Cholangiocytes_KO_vs_WT Platelet activation, signaling and aggregation REAC:R-MMU-76002 18 239 0.0753 0.000827 Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Rhob,F2,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1
DE_genes_Cholangiocytes_KO_vs_WT AUF1 (hnRNP D0) binds and destabilizes mRNA REAC:R-MMU-450408 9 58 0.155 0.00092 Ubc,Psmd8,Hspa8,Hspb1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Antigen processing-Cross presentation REAC:R-MMU-1236975 11 95 0.116 0.00141 H2-T23,H2-Q6,Psmd8,H2-Q7,H2-K1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Itgav
DE_genes_Cholangiocytes_KO_vs_WT Integrin cell surface interactions REAC:R-MMU-216083 9 67 0.134 0.00314 Vtn,Vcam1,Fgg,Col18a1,Fn1,Fga,Itgav,Icam1,Col4a1
DE_genes_Cholangiocytes_KO_vs_WT Regulation of mRNA stability by proteins that bind AU-rich elements REAC:R-MMU-450531 10 85 0.118 0.00336 Ubc,Psmd8,Hspa8,Hspb1,Psmb3,Zfp36,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Autodegradation of the E3 ubiquitin ligase COP1 REAC:R-MMU-349425 8 54 0.148 0.00474 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53
DE_genes_Cholangiocytes_KO_vs_WT Stabilization of p53 REAC:R-MMU-69541 8 58 0.138 0.00812 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53
DE_genes_Cholangiocytes_KO_vs_WT Activation of NF-kappaB in B cells REAC:R-MMU-1169091 8 64 0.125 0.0168 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Nfkbia
DE_genes_Cholangiocytes_KO_vs_WT p53-Dependent G1 DNA Damage Response REAC:R-MMU-69563 8 67 0.119 0.0235 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53
DE_genes_Cholangiocytes_KO_vs_WT p53-Dependent G1/S DNA damage checkpoint REAC:R-MMU-69580 8 67 0.119 0.0235 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53
DE_genes_Cholangiocytes_KO_vs_WT G1/S DNA Damage Checkpoints REAC:R-MMU-69615 8 69 0.116 0.0291 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53
DE_genes_Cholangiocytes_KO_vs_WT Regulation of RUNX2 expression and activity REAC:R-MMU-8939902 7 53 0.132 0.0349 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Ubiquitin-dependent degradation of Cyclin D REAC:R-MMU-75815 7 53 0.132 0.0349 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Hemostasis REAC:R-MMU-109582 26 561 0.0463 0.0353 Trf,Atp1b1,Kif12,Rab27b,Gas6,Ahsg,Cd74,Vegfa,Alb,Serpind1,Apob,Sparc,Rad51b,Rhob,F2,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Mif,Fgg,Fn1,Fga,Igf1,Itgav
DE_genes_Cholangiocytes_KO_vs_WT p53-Independent DNA Damage Response REAC:R-MMU-69610 7 54 0.13 0.0394 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT p53-Independent G1/S DNA damage checkpoint REAC:R-MMU-69613 7 54 0.13 0.0394 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Ubiquitin Mediated Degradation of Phosphorylated Cdc25A REAC:R-MMU-69601 7 54 0.13 0.0394 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT MAPK6/MAPK4 signaling REAC:R-MMU-5687128 8 74 0.108 0.0479 Ubc,Psmd8,Hspb1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Regulation of RUNX3 expression and activity REAC:R-MMU-8941858 7 56 0.125 0.0499 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Cholangiocytes_KO_vs_WT Degradation of AXIN REAC:R-MMU-4641257 7 56 0.125 0.0499 Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3
DE_genes_Endothelial_KO_vs_WT PPAR signaling pathway KEGG:03320 8 89 0.0899 8.07e-05 Fabp1,Apoa2,Cd36,Apoc3,Apoa1,Scp2,Acaa1b,Dbi
DE_genes_Endothelial_KO_vs_WT Metabolic pathways KEGG:01100 31 1531 0.0202 0.000161 Ass1,Gnmt,Gsta3,Hpd,Aldob,Alad,Car3,Gpx1,Rgn,Mat1a,Fbp1,Cth,Scp2,Uox,Arg1,Asl,Acaa1b,Urah,Atp5e,Otc,Cdo1,Pcbd1,mt-Nd4l,Gstm1,Cyp26b1,Tst,Adk,Prdx6,Sephs2,Mgst1,Oat
DE_genes_Endothelial_KO_vs_WT Fluid shear stress and atherosclerosis KEGG:05418 9 141 0.0638 0.000295 Actg1,Ass1,Gsta3,Ctsl,Cyba,Il1a,Klf2,Gstm1,Mgst1
DE_genes_Endothelial_KO_vs_WT Biosynthesis of amino acids KEGG:01230 7 77 0.0909 0.00037 Ass1,Aldob,Mat1a,Cth,Arg1,Asl,Otc
DE_genes_Endothelial_KO_vs_WT Arginine biosynthesis KEGG:00220 4 20 0.2 0.00195 Ass1,Arg1,Asl,Otc
DE_genes_Endothelial_KO_vs_WT Cholesterol metabolism KEGG:04979 5 49 0.102 0.00528 Apoa2,Cd36,Apoc3,Apoc1,Apoa1
DE_genes_Endothelial_KO_vs_WT Glutathione metabolism KEGG:00480 5 68 0.0735 0.0253 Gsta3,Gpx1,Gstm1,Prdx6,Mgst1
DE_genes_Endothelial_KO_vs_WT Metabolism REAC:R-MMU-1430728 40 1678 0.0238 2.1e-09 Fabp1,Alb,Apoa2,Cd36,Ass1,Gnmt,Gsta3,Hpd,Gpihbp1,Ttr,Aldob,Rida,Alad,Rbp4,Car3,Gpx1,Mat1a,Apoa1,Thrsp,Stard10,Fbp1,Cth,Gc,Scp2,Arg1,Asl,Akr1c6,Lyve1,Atp5e,Otc,Cdo1,Pcbd1,Phyh,Cyp26b1,Tst,Adk,Sephs2,Dbi,Mgst1,Oat
DE_genes_Endothelial_KO_vs_WT Platelet degranulation REAC:R-MMU-114608 11 110 0.1 3.44e-07 Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,Apoa1,Ahsg,Lgals3bp
DE_genes_Endothelial_KO_vs_WT Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 11 115 0.0957 5.55e-07 Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,Apoa1,Ahsg,Lgals3bp
DE_genes_Endothelial_KO_vs_WT Metabolism of amino acids and derivatives REAC:R-MMU-71291 14 240 0.0583 1.99e-06 Ass1,Gnmt,Hpd,Rida,Mat1a,Cth,Arg1,Asl,Otc,Cdo1,Pcbd1,Tst,Sephs2,Oat
DE_genes_Endothelial_KO_vs_WT Platelet activation, signaling and aggregation REAC:R-MMU-76002 12 239 0.0502 0.000136 Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,F2r,Apoa1,Ahsg,Lgals3bp
DE_genes_Endothelial_KO_vs_WT Urea cycle REAC:R-MMU-70635 4 10 0.4 0.000235 Ass1,Arg1,Asl,Otc
DE_genes_Endothelial_KO_vs_WT Retinoid metabolism and transport REAC:R-MMU-975634 6 44 0.136 0.000387 Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6
DE_genes_Endothelial_KO_vs_WT Metabolism of fat-soluble vitamins REAC:R-MMU-6806667 6 49 0.122 0.000742 Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6
DE_genes_Endothelial_KO_vs_WT Collagen degradation REAC:R-MMU-1442490 6 53 0.113 0.00119 Ctsl,Ctsb,Col4a2,Col4a1,Mmp14,Col5a2
DE_genes_Endothelial_KO_vs_WT Plasma lipoprotein assembly, remodeling, and clearance REAC:R-MMU-174824 6 58 0.103 0.00202 Alb,Apoa2,Gpihbp1,Apoc1,Apoa1,Apoc4
DE_genes_Endothelial_KO_vs_WT Plasma lipoprotein assembly REAC:R-MMU-8963898 4 18 0.222 0.00326 Apoa2,Apoc1,Apoa1,Apoc4
DE_genes_Endothelial_KO_vs_WT Metabolism of porphyrins REAC:R-MMU-189445 4 23 0.174 0.00913 Fabp1,Alb,Gsta3,Alad
DE_genes_Endothelial_KO_vs_WT Extracellular matrix organization REAC:R-MMU-1474244 10 253 0.0395 0.0108 Sparc,Ttr,Ctsl,Ctsb,Emilin1,Col4a2,Col4a1,Icam2,Mmp14,Col5a2
DE_genes_Endothelial_KO_vs_WT Sulfur amino acid metabolism REAC:R-MMU-1614635 4 24 0.167 0.0109 Mat1a,Cth,Cdo1,Tst
DE_genes_Endothelial_KO_vs_WT Plasma lipoprotein remodeling REAC:R-MMU-8963899 4 25 0.16 0.0129 Alb,Apoa2,Gpihbp1,Apoa1
DE_genes_Endothelial_KO_vs_WT Chylomicron remodeling REAC:R-MMU-8963901 3 10 0.3 0.0168 Apoa2,Gpihbp1,Apoa1
DE_genes_Endothelial_KO_vs_WT Assembly of collagen fibrils and other multimeric structures REAC:R-MMU-2022090 5 54 0.0926 0.021 Ctsl,Ctsb,Col4a2,Col4a1,Col5a2
DE_genes_Endothelial_KO_vs_WT Trafficking and processing of endosomal TLR REAC:R-MMU-1679131 3 11 0.273 0.023 Ctsl,Lgmn,Ctsb
DE_genes_Endothelial_KO_vs_WT Visual phototransduction REAC:R-MMU-2187338 6 91 0.0659 0.0269 Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6
DE_genes_Endothelial_KO_vs_WT Heme degradation REAC:R-MMU-189483 3 12 0.25 0.0305 Fabp1,Alb,Gsta3
DE_genes_Endothelial_KO_vs_WT Degradation of cysteine and homocysteine REAC:R-MMU-1614558 3 12 0.25 0.0305 Cth,Cdo1,Tst
DE_genes_Endothelial_KO_vs_WT Non-integrin membrane-ECM interactions REAC:R-MMU-3000171 4 34 0.118 0.0446 Ttr,Col4a2,Col4a1,Col5a2
DE_genes_Hepatocytes_KO_vs_WT Metabolic pathways KEGG:01100 77 1531 0.0503 9.87e-17 Selenbp2,Aox3,Car3,Hpd,Asl,Mat1a,Gstt3,Pck1,Cyp2e1,Gnmt,Elovl3,Got1,Alas2,Nnmt,Ass1,Aldob,Cth,Gsta2,Gstm3,Gstm1,Hsd3b5,Cbr1,Aldh2,Nme2,Hao2,Gm3776,Keg1,Rdh16f2,Acnat2,Pank1,Acot3,Gstk1,Gls2,Acot1,Cyp3a11,Alas1,Papss2,Tat,Acaa1b,Gstt1,Cyp4a12a,Cyp2c40,Fbp1,Kyat3,Alad,Acadl,Cyp3a44,Oat,Cyp2a4,Mgst1,Gsta1,Sds,Upp2,Ugp2,Acot4,Grhpr,Car5a,Hadh,Cyp2c50,Mocs2,Aass,Nadk,Selenbp1,Me1,Paics,Acmsd,Nat8f2,Cyp2a5,Sord,Agmat,Aldh8a1,Aldh3a2,Akr1d1,Etnppl,Coq7,Hao1,Gclc
DE_genes_Hepatocytes_KO_vs_WT Chemical carcinogenesis KEGG:05204 20 96 0.208 5.36e-14 Gstt3,Sult2a5,Sult2a1,Cyp2e1,Sult1a1,Gsta2,Gstm3,Gstm1,Cbr1,Gm3776,Gstk1,Cyp3a11,Gstt1,Cyp2c40,Kyat3,Cyp3a44,Mgst1,Gsta1,Cyp2c50,Sult2a8
DE_genes_Hepatocytes_KO_vs_WT Drug metabolism - cytochrome P450 KEGG:00982 14 67 0.209 1.51e-09 Aox3,Gstt3,Cyp2e1,Fmo3,Gsta2,Gstm3,Gstm1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Fmo1,Fmo2
DE_genes_Hepatocytes_KO_vs_WT Metabolism of xenobiotics by cytochrome P450 KEGG:00980 14 69 0.203 2.3e-09 Gstt3,Sult2a5,Sult2a1,Cyp2e1,Gsta2,Gstm3,Gstm1,Cbr1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Sult2a8
DE_genes_Hepatocytes_KO_vs_WT Glutathione metabolism KEGG:00480 11 68 0.162 4.22e-06 Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Nat8f2,Gclc
DE_genes_Hepatocytes_KO_vs_WT Drug metabolism - other enzymes KEGG:00983 12 88 0.136 7.26e-06 Gstt3,Cyp2e1,Gsta2,Gstm3,Gstm1,Nme2,Gm3776,Gstt1,Mgst1,Gsta1,Upp2,Tpmt
DE_genes_Hepatocytes_KO_vs_WT Biosynthesis of cofactors KEGG:01240 15 150 0.1 1.14e-05 Hpd,Mat1a,Alas2,Aldh2,Nme2,Pank1,Alas1,Alad,Ugp2,Mocs2,Nadk,Ak3,Aldh3a2,Coq7,Gclc
DE_genes_Hepatocytes_KO_vs_WT Fluid shear stress and atherosclerosis KEGG:05418 13 141 0.0922 0.000209 Gstt3,Ass1,Hsp90ab1,Gsta2,Gstm3,Gstm1,Jun,Gm3776,Actb,Gstt1,Mgst1,Gsta1,Actg1
DE_genes_Hepatocytes_KO_vs_WT Platinum drug resistance KEGG:01524 9 76 0.118 0.00108 Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Cdkn1a,Gstt1,Mgst1,Gsta1
DE_genes_Hepatocytes_KO_vs_WT Peroxisome KEGG:04146 9 84 0.107 0.00245 Nudt7,Hacl1,Ech1,Hao2,Acnat2,Gstk1,Acaa1b,Prdx5,Hao1
DE_genes_Hepatocytes_KO_vs_WT Biosynthesis of unsaturated fatty acids KEGG:01040 6 34 0.176 0.00334 Elovl3,Acnat2,Acot3,Acot1,Acaa1b,Acot4
DE_genes_Hepatocytes_KO_vs_WT Steroid hormone biosynthesis KEGG:00140 9 88 0.102 0.00357 Cyp2e1,Hsd3b5,Cyp2d9,Cyp3a11,Cyp2c40,Cyp3a44,Cyp2d40,Cyp2c50,Akr1d1
DE_genes_Hepatocytes_KO_vs_WT Tryptophan metabolism KEGG:00380 7 51 0.137 0.00401 Aox3,Aldh2,Kyat3,Hadh,Acmsd,Aldh8a1,Aldh3a2
DE_genes_Hepatocytes_KO_vs_WT Cysteine and methionine metabolism KEGG:00270 7 51 0.137 0.00401 Mat1a,Got1,Cth,Tat,Kyat3,Sds,Gclc
DE_genes_Hepatocytes_KO_vs_WT Retinol metabolism KEGG:00830 9 94 0.0957 0.00604 Aox3,Rdh16f2,Cyp3a11,Cyp4a12a,Cyp2c40,Cyp3a44,Cyp2a4,Cyp2c50,Cyp2a5
DE_genes_Hepatocytes_KO_vs_WT Glycine, serine and threonine metabolism KEGG:00260 6 38 0.158 0.00644 Gnmt,Alas2,Cth,Alas1,Sds,Grhpr
DE_genes_Hepatocytes_KO_vs_WT Fatty acid elongation KEGG:00062 5 29 0.172 0.0174 Elovl3,Acot3,Acot1,Acot4,Hadh
DE_genes_Hepatocytes_KO_vs_WT Hepatocellular carcinoma KEGG:05225 11 165 0.0667 0.0253 Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Cdkn1a,Actb,Gstt1,Mgst1,Gsta1,Actg1
DE_genes_Hepatocytes_KO_vs_WT Complement and coagulation cascades KEGG:04610 8 91 0.0879 0.0282 Serpina1d,Serpina1c,Serpina1a,Serpina1b,Clu,C4bp,Vtn,Fgb
DE_genes_Hepatocytes_KO_vs_WT Fatty acid degradation KEGG:00071 6 51 0.118 0.0344 Aldh2,Acaa1b,Cyp4a12a,Acadl,Hadh,Aldh3a2
DE_genes_Hepatocytes_KO_vs_WT Arginine biosynthesis KEGG:00220 4 20 0.2 0.0442 Asl,Got1,Ass1,Gls2
DE_genes_Hepatocytes_KO_vs_WT Metabolism REAC:R-MMU-1430728 77 1678 0.0459 5.52e-19 Nudt7,Car3,Hpd,Asl,Mat1a,Thrsp,Pck1,Cyp2e1,Gnmt,Elovl3,Got1,Alas2,Nnmt,Ass1,Aldob,Alb,Fmo3,Hsp90ab1,Cth,Hsd3b5,Fabp5,Rida,Cbr1,Aldh2,Hacl1,Nme2,Hao2,Hpgd,Rbp1,Pank1,Acot3,Gstk1,Gls2,Acot1,Cyp3a11,Alas1,Papss2,Tat,Gstt1,Cyp4a12a,Fbp1,Akr1c6,Alad,Cyp3a44,Oat,Fitm1,Cyp2a4,Mgst1,Apoa1,Gsta1,Sds,Upp2,Ugp2,Acot4,Grhpr,Car5a,Hadh,Slc25a15,Aass,Nadk,Me1,Paics,Fmo1,Gchfr,Fmo2,Sord,Agmat,Pon1,Aldh3a2,Akr1d1,As3mt,Tstd1,Etnppl,Hao1,Gclc,Psmb8,Apoe
DE_genes_Hepatocytes_KO_vs_WT Biological oxidations REAC:R-MMU-211859 20 204 0.098 1.95e-08 Mat1a,Cyp2e1,Nnmt,Fmo3,Hsp90ab1,Aldh2,Gstk1,Cyp3a11,Papss2,Gstt1,Cyp4a12a,Cyp3a44,Cyp2a4,Mgst1,Gsta1,Ugp2,Fmo1,Fmo2,As3mt,Gclc
DE_genes_Hepatocytes_KO_vs_WT Protein localization REAC:R-MMU-9609507 14 100 0.14 1.58e-07 Nudt7,Hacl1,Ech1,Hao2,Hspd1,Ubb,Acot3,Gstk1,Acot1,Sec61g,Acot4,Sec61b,Aldh3a2,Hao1
DE_genes_Hepatocytes_KO_vs_WT Metabolism of amino acids and derivatives REAC:R-MMU-71291 19 240 0.0792 2.29e-06 Hpd,Asl,Mat1a,Gnmt,Got1,Ass1,Cth,Rida,Gls2,Tat,Oat,Sds,Grhpr,Slc25a15,Aass,Agmat,Tstd1,Hao1,Psmb8
DE_genes_Hepatocytes_KO_vs_WT Peroxisomal protein import REAC:R-MMU-9033241 10 63 0.159 1.53e-05 Nudt7,Hacl1,Ech1,Hao2,Ubb,Acot3,Gstk1,Acot1,Acot4,Hao1
DE_genes_Hepatocytes_KO_vs_WT Fatty acid metabolism REAC:R-MMU-8978868 14 168 0.0833 0.000133 Nudt7,Thrsp,Elovl3,Cbr1,Hacl1,Hao2,Acot3,Acot1,Cyp4a12a,Akr1c6,Acot4,Hadh,Pon1,Aldh3a2
DE_genes_Hepatocytes_KO_vs_WT Phase II - Conjugation of compounds REAC:R-MMU-156580 10 92 0.109 0.000581 Mat1a,Nnmt,Gstk1,Papss2,Gstt1,Mgst1,Gsta1,Ugp2,As3mt,Gclc
DE_genes_Hepatocytes_KO_vs_WT FMO oxidises nucleophiles REAC:R-MMU-217271 3 3 1 0.00124 Fmo3,Fmo1,Fmo2
DE_genes_Hepatocytes_KO_vs_WT Phase I - Functionalization of compounds REAC:R-MMU-211945 10 106 0.0943 0.00212 Cyp2e1,Fmo3,Hsp90ab1,Aldh2,Cyp3a11,Cyp4a12a,Cyp3a44,Cyp2a4,Fmo1,Fmo2
DE_genes_Hepatocytes_KO_vs_WT Heme biosynthesis REAC:R-MMU-189451 4 12 0.333 0.00869 Alas2,Alb,Alas1,Alad
DE_genes_Hepatocytes_KO_vs_WT Platelet degranulation REAC:R-MMU-114608 9 110 0.0818 0.0194 Alb,Anxa5,Apoa1,Tagln2,Clu,Tmsb4x,Rarres2,Actg1,Fgb
DE_genes_Hepatocytes_KO_vs_WT Peroxisomal lipid metabolism REAC:R-MMU-390918 5 29 0.172 0.0263 Nudt7,Hacl1,Hao2,Acot4,Aldh3a2
DE_genes_Hepatocytes_KO_vs_WT Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 9 115 0.0783 0.0275 Alb,Anxa5,Apoa1,Tagln2,Clu,Tmsb4x,Rarres2,Actg1,Fgb
DE_genes_Hepatocytes_KO_vs_WT Metabolism of lipids REAC:R-MMU-556833 22 583 0.0377 0.041 Nudt7,Thrsp,Cyp2e1,Elovl3,Alb,Hsd3b5,Fabp5,Cbr1,Hacl1,Hao2,Hpgd,Acot3,Acot1,Cyp4a12a,Akr1c6,Fitm1,Acot4,Hadh,Pon1,Aldh3a2,Akr1d1,Etnppl
DE_genes_Hepatocytes_KO_vs_WT Glutathione conjugation REAC:R-MMU-156590 5 32 0.156 0.0429 Gstk1,Gstt1,Mgst1,Gsta1,Gclc
DE_genes_HSC & PF_KO_vs_WT Focal adhesion KEGG:04510 19 196 0.0969 1.07e-05 Itga8,Actg1,Pdgfrb,Mylk,Col4a2,Actb,Col6a1,Col6a3,Col6a2,Col1a1,Igf1,Vasp,Vegfc,Col4a1,Actn1,Fn1,Ccnd2,Col6a5,Kdr
DE_genes_HSC & PF_KO_vs_WT Fluid shear stress and atherosclerosis KEGG:05418 15 141 0.106 7.51e-05 Actg1,Gsta3,Actb,Ass1,Il1r1,Mmp2,Tnfrsf1a,Vcam1,Sdc2,Hmox1,Fos,Sdc4,Dusp1,Kdr,Klf2
DE_genes_HSC & PF_KO_vs_WT ECM-receptor interaction KEGG:04512 10 87 0.115 0.00277 Itga8,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Sdc4,Fn1,Col6a5
DE_genes_HSC & PF_KO_vs_WT PPAR signaling pathway KEGG:03320 10 89 0.112 0.00339 Lpl,Fabp1,Apoa2,Hmgcs2,Acaa1b,Apoc3,Scp2,Apoa1,Dbi,Fabp4
DE_genes_HSC & PF_KO_vs_WT Complement and coagulation cascades KEGG:04610 10 91 0.11 0.00411 Serpina1c,C4b,Serpina1a,Masp1,Pros1,C6,C3,Cfb,Cd59a,Serpina1b
DE_genes_HSC & PF_KO_vs_WT Cholesterol metabolism KEGG:04979 7 49 0.143 0.0112 Lpl,Apoe,Apoa2,Vdac2,Apoc3,Apoc1,Apoa1
DE_genes_HSC & PF_KO_vs_WT AGE-RAGE signaling pathway in diabetic complications KEGG:04933 9 99 0.0909 0.0424 Col3a1,Col4a2,Col1a1,Mmp2,Vcam1,Vegfc,Col4a1,Egr1,Fn1
DE_genes_HSC & PF_KO_vs_WT Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 25 111 0.225 2.68e-16 C4b,Apoe,Sparcl1,Cst3,Scg2,Scg3,Chgb,Apoa2,Gas6,Cp,Igf1,Igfbp4,Fstl1,Mxra8,Alb,Sdc2,Igfbp6,Timp1,Ltbp1,C3,Apoa1,Fn1,Igfbp5,Ahsg,Igfbp3
DE_genes_HSC & PF_KO_vs_WT Post-translational protein phosphorylation REAC:R-MMU-8957275 23 105 0.219 1.41e-14 C4b,Apoe,Sparcl1,Cst3,Scg2,Scg3,Chgb,Apoa2,Gas6,Cp,Igfbp4,Fstl1,Mxra8,Alb,Sdc2,Timp1,Ltbp1,C3,Apoa1,Fn1,Igfbp5,Ahsg,Igfbp3
DE_genes_HSC & PF_KO_vs_WT Platelet degranulation REAC:R-MMU-114608 21 110 0.191 6.74e-12 Islr,Actg1,Scg3,Lamp2,Gas6,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1
DE_genes_HSC & PF_KO_vs_WT Extracellular matrix organization REAC:R-MMU-1474244 30 253 0.119 9.16e-12 Lum,Itga8,Col3a1,Serpinh1,Emilin1,Fbln5,Ttr,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Ppib,Adamts5,Sparc,Efemp2,Adamts2,Htra1,Jam2,Vcam1,Mmp14,Sdc2,Col4a1,Col5a2,Ctsk,Timp1,Ltbp1,Sdc4,Fn1
DE_genes_HSC & PF_KO_vs_WT Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 21 115 0.183 1.71e-11 Islr,Actg1,Scg3,Lamp2,Gas6,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1
DE_genes_HSC & PF_KO_vs_WT Integrin cell surface interactions REAC:R-MMU-216083 13 67 0.194 6.18e-07 Lum,Itga8,Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Jam2,Vcam1,Col4a1,Col5a2,Fn1
DE_genes_HSC & PF_KO_vs_WT Platelet activation, signaling and aggregation REAC:R-MMU-76002 23 239 0.0962 8.14e-07 Islr,Actg1,Scg3,Lamp2,Col1a1,Gas6,Rhob,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1
DE_genes_HSC & PF_KO_vs_WT Collagen degradation REAC:R-MMU-1442490 11 53 0.208 5.42e-06 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Mmp14,Col4a1,Col5a2,Ctsk
DE_genes_HSC & PF_KO_vs_WT Non-integrin membrane-ECM interactions REAC:R-MMU-3000171 9 34 0.265 1.17e-05 Col3a1,Ttr,Col4a2,Col1a1,Sdc2,Col4a1,Col5a2,Sdc4,Fn1
DE_genes_HSC & PF_KO_vs_WT Collagen biosynthesis and modifying enzymes REAC:R-MMU-1650814 11 59 0.186 1.77e-05 Col3a1,Serpinh1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Ppib,Adamts2,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT Degradation of the extracellular matrix REAC:R-MMU-1474228 15 121 0.124 2.04e-05 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Adamts5,Htra1,Mmp14,Col4a1,Col5a2,Ctsk,Timp1,Fn1
DE_genes_HSC & PF_KO_vs_WT NCAM1 interactions REAC:R-MMU-419037 7 18 0.389 2.07e-05 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT ECM proteoglycans REAC:R-MMU-3000178 9 40 0.225 5.46e-05 Itga8,Col3a1,Col6a1,Col6a3,Col6a2,Col1a1,Sparc,Col5a2,Fn1
DE_genes_HSC & PF_KO_vs_WT NCAM signaling for neurite out-growth REAC:R-MMU-375165 8 34 0.235 0.000189 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2,Sptbn1
DE_genes_HSC & PF_KO_vs_WT Collagen formation REAC:R-MMU-1474290 11 79 0.139 0.000389 Col3a1,Serpinh1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Ppib,Adamts2,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT Collagen chain trimerization REAC:R-MMU-8948216 8 38 0.211 0.000471 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT Retinoid metabolism and transport REAC:R-MMU-975634 8 44 0.182 0.00152 Lpl,Apoe,Ttr,Apoa2,Rbp4,Sdc2,Sdc4,Apoa1
DE_genes_HSC & PF_KO_vs_WT Hemostasis REAC:R-MMU-109582 30 561 0.0535 0.00175 H3f3b,Islr,Actg1,Scg3,Lamp2,Col1a1,Gas6,Rhob,Igf1,Cd9,Epcam,Sparc,Tagln2,Cd63,Alb,Jam2,Vegfc,Sdc2,Selenop,Pros1,Pf4,Actn1,Timp1,Sdc4,Apoa1,Fn1,Ahsg,Ehd3,Ecm1,Cd74
DE_genes_HSC & PF_KO_vs_WT Metabolism of fat-soluble vitamins REAC:R-MMU-6806667 8 49 0.163 0.00353 Lpl,Apoe,Ttr,Apoa2,Rbp4,Sdc2,Sdc4,Apoa1
DE_genes_HSC & PF_KO_vs_WT Cell-extracellular matrix interactions REAC:R-MMU-446353 5 15 0.333 0.00434 Actg1,Actb,Vasp,Actn1,Fblim1
DE_genes_HSC & PF_KO_vs_WT Nervous system development REAC:R-MMU-9675108 18 256 0.0703 0.00469 Col3a1,Actg1,Col4a2,Actb,Col6a1,Cxcl12,Col6a3,Col6a2,Gfra2,Rhob,Mmp2,Vasp,Sdc2,Col4a1,Col5a2,Plxna4,Sptbn1,Ezr
DE_genes_HSC & PF_KO_vs_WT Axon guidance REAC:R-MMU-422475 18 256 0.0703 0.00469 Col3a1,Actg1,Col4a2,Actb,Col6a1,Cxcl12,Col6a3,Col6a2,Gfra2,Rhob,Mmp2,Vasp,Sdc2,Col4a1,Col5a2,Plxna4,Sptbn1,Ezr
DE_genes_HSC & PF_KO_vs_WT Signaling by PDGF REAC:R-MMU-186797 8 52 0.154 0.00557 Col3a1,Pdgfrb,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT Assembly of collagen fibrils and other multimeric structures REAC:R-MMU-2022090 8 54 0.148 0.00741 Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Col5a2
DE_genes_HSC & PF_KO_vs_WT Plasma lipoprotein assembly REAC:R-MMU-8963898 5 18 0.278 0.0117 Apoe,Apoa2,Apoc4,Apoc1,Apoa1
DE_genes_HSC & PF_KO_vs_WT Chylomicron remodeling REAC:R-MMU-8963901 4 10 0.4 0.0151 Lpl,Apoe,Apoa2,Apoa1
DE_genes_HSC & PF_KO_vs_WT Molecules associated with elastic fibres REAC:R-MMU-2129379 6 31 0.194 0.0173 Itga8,Emilin1,Fbln5,Efemp2,Ltbp1,Fn1
DE_genes_HSC & PF_KO_vs_WT Heme degradation REAC:R-MMU-189483 4 12 0.333 0.0344 Fabp1,Gsta3,Alb,Hmox1
DE_genes_HSC & PF_KO_vs_WT Metabolism of porphyrins REAC:R-MMU-189445 5 23 0.217 0.0421 Fabp1,Alad,Gsta3,Alb,Hmox1
DE_genes_HSC & PF_KO_vs_WT Elastic fibre formation REAC:R-MMU-1566948 6 37 0.162 0.0489 Itga8,Emilin1,Fbln5,Efemp2,Ltbp1,Fn1
DE_genes_Macrophage_Kupffer_KO_vs_WT Complement and coagulation cascades KEGG:04610 9 91 0.0989 4.27e-05 C6,C4b,Cfh,C2,Serpina1c,Vsig4,Clu,Serpina1a,Serpina1b
DE_genes_Macrophage_Kupffer_KO_vs_WT Staphylococcus aureus infection KEGG:05150 9 116 0.0776 0.000333 C4b,Fpr1,Cfh,C2,Itgal,Krt18,H2-Ab1,H2-Aa,H2-Eb1
DE_genes_Macrophage_Kupffer_KO_vs_WT PPAR signaling pathway KEGG:03320 8 89 0.0899 0.000396 Apoa2,Cd36,Rxra,Fabp5,Apoc3,Lpl,Fabp1,Apoa1
DE_genes_Macrophage_Kupffer_KO_vs_WT Phagosome KEGG:04145 10 173 0.0578 0.00132 Cd209g,Cd209f,H2-D1,Cd36,Mrc1,Tubb5,Coro1a,H2-Ab1,H2-Aa,H2-Eb1
DE_genes_Macrophage_Kupffer_KO_vs_WT Tuberculosis KEGG:05152 10 179 0.0559 0.00177 Cd209g,Cd209f,Mrc1,Ifngr1,Ctsd,Lsp1,Coro1a,H2-Ab1,H2-Aa,H2-Eb1
DE_genes_Macrophage_Kupffer_KO_vs_WT Viral protein interaction with cytokine and cytokine receptor KEGG:04061 7 92 0.0761 0.0048 Ccl6,Cxcl13,Ccr3,Ccl24,Cx3cr1,Cxcl14,Ccr2
DE_genes_Macrophage_Kupffer_KO_vs_WT Epstein-Barr virus infection KEGG:05169 10 221 0.0452 0.0106 B2m,H2-D1,Itgal,Hes1,Blnk,Vim,Gadd45b,H2-Ab1,H2-Aa,H2-Eb1
DE_genes_Macrophage_Kupffer_KO_vs_WT Cholesterol metabolism KEGG:04979 5 49 0.102 0.0148 Apoa2,Cd36,Apoc3,Lpl,Apoa1
DE_genes_Macrophage_Kupffer_KO_vs_WT Inflammatory bowel disease KEGG:05321 5 61 0.082 0.0418 Maf,Ifngr1,H2-Ab1,H2-Aa,H2-Eb1
DE_genes_Macrophage_Kupffer_KO_vs_WT Neutrophil degranulation REAC:R-MMU-6798695 22 517 0.0426 7.63e-07 Cd63,B2m,Fcna,Ctsc,Cfp,Fpr1,Lilra5,Anxa2,Cd36,Fabp5,Pira2,Itgal,Nme2,Ctsd,Cstb,Hexb,Gsn,Fth1,Cd300c2,Tubb5,Vat1,Plac8
DE_genes_Macrophage_Kupffer_KO_vs_WT Innate Immune System REAC:R-MMU-168249 30 976 0.0307 1.15e-06 Cd63,C6,B2m,Fcna,C4b,Ctsc,Cfp,Fpr1,Cfh,Lilra5,Txnip,Anxa2,Cd36,C2,Fabp5,Pira2,Itgal,Nme2,Ctsd,Cstb,Clu,Hexb,Gsn,Fth1,Cd300c2,Pld3,Tubb5,Ctnnb1,Vat1,Plac8
DE_genes_Macrophage_Kupffer_KO_vs_WT Post-translational protein phosphorylation REAC:R-MMU-8957275 10 105 0.0952 1.83e-05 C4b,Lgals1,Trf,Alb,Apoa2,Spp1,Fam20c,Apoa1,Ccn1,Cp
DE_genes_Macrophage_Kupffer_KO_vs_WT Platelet degranulation REAC:R-MMU-114608 10 110 0.0909 2.86e-05 Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc
DE_genes_Macrophage_Kupffer_KO_vs_WT Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) REAC:R-MMU-381426 10 111 0.0901 3.12e-05 C4b,Lgals1,Trf,Alb,Apoa2,Spp1,Fam20c,Apoa1,Ccn1,Cp
DE_genes_Macrophage_Kupffer_KO_vs_WT Response to elevated platelet cytosolic Ca2+ REAC:R-MMU-76005 10 115 0.087 4.37e-05 Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc
DE_genes_Macrophage_Kupffer_KO_vs_WT Chylomicron remodeling REAC:R-MMU-8963901 4 10 0.4 0.000493 Apoa2,Lpl,Apoa1,Gpihbp1
DE_genes_Macrophage_Kupffer_KO_vs_WT Plasma lipoprotein remodeling REAC:R-MMU-8963899 5 25 0.2 0.00104 Alb,Apoa2,Lpl,Apoa1,Gpihbp1
DE_genes_Macrophage_Kupffer_KO_vs_WT Immune System REAC:R-MMU-168256 35 1737 0.0201 0.00171 Cd63,C6,B2m,Fcna,C4b,Ctsc,Cfp,Fpr1,Cfh,Lilra5,Txnip,Anxa2,Cd36,C2,Fabp5,Mrc1,Pira2,Itgal,Nme2,Ifngr1,Ctsd,Cstb,Clu,Hexb,Il1rn,Gsn,Fth1,Cd300c2,Pld3,Blnk,Tubb5,Ctnnb1,Vat1,Dusp1,Plac8
DE_genes_Macrophage_Kupffer_KO_vs_WT Activation of C3 and C5 REAC:R-MMU-174577 3 7 0.429 0.00885 C4b,Cfp,C2
DE_genes_Macrophage_Kupffer_KO_vs_WT Complement cascade REAC:R-MMU-166658 7 109 0.0642 0.0257 C6,Fcna,C4b,Cfp,Cfh,C2,Clu
DE_genes_Macrophage_Kupffer_KO_vs_WT Platelet activation, signaling and aggregation REAC:R-MMU-76002 10 239 0.0418 0.0304 Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc

2 Methods

For pathway analysis, the R package gprofiler2 v0.2.0 was employed. Graphs were produced in RStudio with R version 4.0.3 (2020-10-10) mainly using the R package ggplot2 v3.3.2. Final reports were produced using the R package rmarkdown v2.6, with knitr v1.30.